Also, try holding the driver while it's thumping, out of the box, turn it on it's side and then try turning it on the other sides.
Ok, that sounded stupid. basically, what I'm getting at is the vc might not be aligned right, and turning it on its side might clear up the noise.
If it does, I'd guess the driver needs to be replaced. Luckily eD is really good about their warranty policy...although it sucks to have problems with a brand new sub, I'll admit.